[med-svn] r1787 - in trunk/packages/tigr-glimmer/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Apr 17 09:06:18 UTC 2008
Author: tille
Date: 2008-04-17 09:06:18 +0000 (Thu, 17 Apr 2008)
New Revision: 1787
Added:
trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch
Modified:
trunk/packages/tigr-glimmer/trunk/debian/patches/series
trunk/packages/tigr-glimmer/trunk/debian/rules
Log:
gcc-4.3 patches
Added: trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch (rev 0)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch 2008-04-17 09:06:18 UTC (rev 1787)
@@ -0,0 +1,172 @@
+--- glimmer3.02.orig/src/Common/delcher.cc
++++ glimmer3.02/src/Common/delcher.cc
+@@ -9,6 +9,7 @@
+
+ #include "delcher.hh"
+
++#include <cstring>
+
+ const int COMMATIZE_BUFF_LEN = 50;
+ // Length of buffer for creating string with commas
+--- glimmer3.02.orig/src/Common/fasta.cc
++++ glimmer3.02/src/Common/fasta.cc
+@@ -9,7 +9,7 @@
+
+ #include "fasta.hh"
+
+-
++#include <cstring>
+
+ void Fasta_Print
+ (FILE * fp, const char * s, const char * hdr, int fasta_width)
+--- glimmer3.02.orig/src/Common/gene.cc
++++ glimmer3.02/src/Common/gene.cc
+@@ -10,6 +10,7 @@
+ #include "delcher.hh"
+ #include "gene.hh"
+
++#include <cstring>
+
+ static const char COMPLEMENT_TABLE []
+ = "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
+--- glimmer3.02.orig/src/Glimmer/anomaly.cc
++++ glimmer3.02/src/Glimmer/anomaly.cc
+@@ -12,6 +12,7 @@
+
+ #include "anomaly.hh"
+
++#include <cstring>
+
+ // Global variables
+
+--- glimmer3.02.orig/src/ICM/icm.cc
++++ glimmer3.02/src/ICM/icm.cc
+@@ -15,6 +15,8 @@
+
+ #include "icm.hh"
+
++#include <cstring>
++
+ using namespace std;
+
+ extern int Verbose;
+--- glimmer3.02.orig/src/Util/entropy-score.cc
++++ glimmer3.02/src/Util/entropy-score.cc
+@@ -9,7 +9,7 @@
+ // regions in it by entropy distance. Results are output
+ // to stdout .
+
+-
++#include <cstring>
+
+ #include "entropy-score.hh"
+
+--- glimmer3.02.orig/src/Glimmer/glimmer3.cc
++++ glimmer3.02/src/Glimmer/glimmer3.cc
+@@ -12,11 +12,10 @@
+ // Copyright (c) 2006 University of Maryland Center for Bioinformatics
+ // & Computational Biology
+
+-
++#include <cstring>
+
+ #include "glimmer3.hh"
+
+-
+ static int For_Edwin = 0;
+
+
+--- glimmer3.02.orig/src/ICM/build-icm.cc
++++ glimmer3.02/src/ICM/build-icm.cc
+@@ -13,6 +13,7 @@
+
+ #include "build-icm.hh"
+
++#include <cstring>
+
+ static int Genbank_Xlate_Code = 0;
+ // Holds the Genbank translation table number that determines
+--- glimmer3.02.orig/src/Util/extract.cc
++++ glimmer3.02/src/Util/extract.cc
+@@ -9,7 +9,7 @@
+ // sequences specified by coordinates. The resulting sequences
+ // are output (in multifasta or two-string format) to stdout.
+
+-
++#include <cstring>
+
+ #include "extract.hh"
+
+--- glimmer3.02.orig/src/Glimmer/glimmer2.cc
++++ glimmer3.02/src/Glimmer/glimmer2.cc
+@@ -37,6 +37,7 @@
+ #include "delcher.h"
+ #include "gene.h"
+
++#include <cstring>
+
+ const int DEFAULT_MIN_GENE_LEN = 90;
+ const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
+--- glimmer3.02.orig/src/Glimmer/long-orfs.cc
++++ glimmer3.02/src/Glimmer/long-orfs.cc
+@@ -15,7 +15,7 @@
+
+ #include "long-orfs.hh"
+
+-
++#include <cstring>
+
+ // External variables
+
+--- glimmer3.02.orig/src/ICM/build-fixed.cc
++++ glimmer3.02/src/ICM/build-fixed.cc
+@@ -12,6 +12,7 @@
+
+ #include "build-fixed.hh"
+
++#include <cstring>
+
+ static FILE * Index_File_fp = NULL;
+ // File containing a list of subscripts of strings to train model
+--- glimmer3.02.orig/src/ICM/score-fixed.cc
++++ glimmer3.02/src/ICM/score-fixed.cc
+@@ -8,6 +8,7 @@
+
+ #include "score-fixed.hh"
+
++#include <cstring>
+
+ static char * Pos_Model_Path;
+ // Name of file containing the positive model
+--- glimmer3.02.orig/src/Util/multi-extract.cc
++++ glimmer3.02/src/Util/multi-extract.cc
+@@ -10,7 +10,7 @@
+ // resulting sequences are output (in multifasta or two-string format)
+ // to stdout.
+
+-
++#include <cstring>
+
+ #include "multi-extract.hh"
+
+--- glimmer3.02.orig/src/Util/start-codon-distrib.cc
++++ glimmer3.02/src/Util/start-codon-distrib.cc
+@@ -17,6 +17,7 @@
+
+ #include "start-codon-distrib.hh"
+
++#include <cstring>
+
+ // External variables
+
+--- glimmer3.02.orig/src/Util/uncovered.cc
++++ glimmer3.02/src/Util/uncovered.cc
+@@ -10,7 +10,7 @@
+ // specified in the file named as the second command-line argument.
+ // Output is a multifasta file sent to stdout.
+
+-
++#include <cstring>
+
+ #include "uncovered.hh"
+
Modified: trunk/packages/tigr-glimmer/trunk/debian/patches/series
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/series 2008-04-16 21:35:35 UTC (rev 1786)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/series 2008-04-17 09:06:18 UTC (rev 1787)
@@ -1 +1,2 @@
01_Makefile.patch
+10_gcc4.3.patch
Modified: trunk/packages/tigr-glimmer/trunk/debian/rules
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/rules 2008-04-16 21:35:35 UTC (rev 1786)
+++ trunk/packages/tigr-glimmer/trunk/debian/rules 2008-04-17 09:06:18 UTC (rev 1787)
@@ -20,6 +20,7 @@
clean::
dh_clean $(MANPAGES)
+ cd src; make clean
rm -f bin/* lib/* obj/*
build/tigr-glimmer:: $(MANPAGES)
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